Software repository

We started a project on benchmarking of software for 3D chromatin organisation – please see here how you can contribute: https://inc-cost.eu/benchmarking

The database below lists software developed by INC members for nucleome data analysis and modeling.

The interactive table below classifies (non-exhaustively) the tools by the following tasks:

  • Hi-C generation: from raw Hi-C data to Hi-C matrices, etc
  • Hi-C analysis: infer/compare compartments, TADs, structural motifs, etc, from Hi-C data.
  • Hi-C visualization: functions to visualize Hi-C data
  • Image analysis: functions to process and analyse images or movies from microscopy
  • Integrative modeling: reconstructions of 3D genome conformations from 4D genomics data
  • Biophysical modeling: bottom-up thermodynamic/mechanistic models to predict chromatin organization
  • Statistical modeling: statistical models to predict contacts, TAD boundaries, structural motifs, etc.
  • Nucleosome analysis: Inferring nucleosome landscapes from sequencing data
Software nameHi-C generationHi-C analysisHi-C visualizationImage analysisIntegrative modelingBiophysical modellingStatistical modellingNucleosome analysis
3DEpiBlock X
3DPredictor X
Binless XX
Chrom3D X
ChromFold X
ChromHL X
CHESS X
C-InterSecture XX
FAN-C XXX
HiCBricksXXX
IC-FinderX
IMGRXX
NRLcalcXX
NucToolsX
TADbitXXXX
TADdynX
TADkitX
TADpoleX
TFaffinityX